11	datasets
73	experiments
2,845	MS runs
176,414,124	spectra searched
22,362,108	PSMs
265,742	distinct peptides
11,482	canonical proteins

About

The Human DIA PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Available datasets of Human samples were reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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All detected canonical proteins

Chromosome Summary

Column descriptions ▲

Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

A publication describing the Human DIA PeptideAtlas build is in progress.

For now, please just reference this URL, and check back later for a citation.

Download

Below are individual Human DIA PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Human DIA 2026-03 PSM FDR = 0.00008Latest Build

Biosequence Set in FASTA format [457MB]
Database tables exported as TSV dump file [193MB]
Database tables exported as mysql dump file [134MB]
Peptide CDS and chromosomal coordinates [614MB]
Peptide CDS coordinates [384MB]
Peptide sequences in FASTA format [5MB]

Help

Complete description of each of the available download formats

Acknowledgements

We gratefully acknowledge the support for the Human DIA PeptideAtlas from National Science Foundation grant DBI-2324882, “Globally harmonized re-analysis of Data Independent Acquisition (DIA) proteomics datasets enables the creation of new resources (DIA-eXchange)” .